Commit f8fa4179 authored by Sebastien Moretti's avatar Sebastien Moretti
Browse files

Version and requirements updates

parent 005e305d
......@@ -56,7 +56,7 @@ my $blast_param = { 'evalue' => 0.05,
###################################################
my $VERSION = '4.0.0';
my $VERSION = '4.0.7';
my $webblast_exe = 'webblast.pl';
my $blast_exe = 'blastall'; # Or wu-blastall for Wu-BLAST; for local blast usage
......@@ -455,17 +455,17 @@ if ( exists($tmpFiles[0]) ){
#STDOUT Log output for our server
if ( -s "$originalMSA.cds" || -s "$originalMSA.out" ){
print "\n\nTERMINATION STATUS: SUCCESS\n";
print "OUTPUT RESULTS\n";
print 'OUTPUT RESULTS', "\n";
print " #### File Type= MSA Format= fasta_CDS Name= $originalMSA.cds\n"
if ( -s "$originalMSA.cds");
if ( -s "$originalMSA.cds" );
print " #### File Type= MSA Format= fasta_CDS+Query Name= $originalMSA.cdsP\n"
if ( -s "$originalMSA.cdsP");
if ( -s "$originalMSA.cdsP" );
print " #### File Type= MSA Format= colored_fasta_CDS Name= $originalMSA.cdsP.html\n"
if ( Views::Html("$originalMSA.cdsP") && -s "$originalMSA.cdsP.html");
if ( Views::Html("$originalMSA.cdsP") && -s "$originalMSA.cdsP.html" );
print " #### File Type= MSA Format= Rejected_seq Name= $originalMSA.out\n"
if ( -s "$originalMSA.out");
if ( -s "$originalMSA.out" );
print " #### File Type= MSA Format= fasta_Exon-Boundaries Name= $originalMSA.boj\n"
if ( -s "$originalMSA.boj" && -s "$originalMSA.cds" && $hideBOJ==0);
if ( -s "$originalMSA.boj" && -s "$originalMSA.cds" && $hideBOJ==0 );
unlink "$cache/web_tempo.result";
}
......@@ -541,9 +541,9 @@ PROTOGENE re-builds the original alignment with nucleotidic information it has g
=item B<Perl 5.6 or better> is required !
=item Standard Perl modules B<lib>, B<strict>, B<warnings>, B<diagnostics>, B<Env> are required
=item Standard Perl modules B<lib>, B<strict>, B<warnings>, B<diagnostics>, B<Carp> are required
=item and some other current ones : B<Getopt::Long>, B<File::Which>, B<File::Copy>, B<Mail::Send>
=item as well as some other current ones : B<Getopt::Long>, B<File::Which>, B<File::Copy>, B<Mail::Send>, B<Time::localtime>, B<LWP::Simple>
=item -
......@@ -557,9 +557,9 @@ PROTOGENE re-builds the original alignment with nucleotidic information it has g
=over 8
=item version 4.0.5
=item version 4.0.7
=item on Aug 02nd, 2011
=item on Aug 13nd, 2011
=back
......@@ -1462,32 +1462,35 @@ sub checkAndCleanStderrFiles{
my %uniq;
open(my $ERRSTD, '<', "$ExonerateStderrFiles");
while(<$ERRSTD>){
# $body .= $_ if ( $_ !~ /^$/ && $_ !~ /Exhaustively generating suboptimal alignments will be very slow/ && $_ !~ /Message: Exhaustive alignment of/ );
%uniq = (%uniq,"$_" => '') if ( $_ !~ /^$/ && $_ !~ /Exhaustively generating suboptimal alignments will be very slow/ && $_ !~ /Message: Exhaustive alignment of/ && $_ !~ /Missing calc_macro for Calc/ && $_ !~ /Warning zero length sequence/ );
%uniq = (%uniq, "$_" => '')
if ( $_ !~ /^$/ && $_ !~ /Exhaustively generating suboptimal alignments will be very slow/
&& $_ !~ /Message: Exhaustive alignment of/ && $_ !~ /Missing calc_macro for Calc/ && $_ !~ /Warning zero length sequence/ );
}
close $ERRSTD;
while( my ($a,$b)=each(%uniq) ){
while( my ($a, $b) = each(%uniq) ){
$body .= $a;
}
if ( $body ne '' && $userEMail =~ /^[\w\_\-\.]+@[\w\_\-\.]+\.[A-Za-z][A-Za-z][A-Za-z]*$/ ){
my $msg = new Mail::Send Subject=>"[Protogene: ${date}_Error]", To=>"$userEMail";
my $msg = new Mail::Send Subject => "[Protogene: ${date}_Error]", To => "$userEMail";
my $fh = $msg->open;
print $fh $body;
$fh->close; # complete the message and send it
}
}
unlink("$ExonerateStderrFiles") if ( $tmp == 0 || $body eq '' );
return;
}
sub checkOutputFiles{
unlink("$originalMSA.cds") if ( -z "$originalMSA.cds" );
unlink("$originalMSA.cdsP") if ( -z "$originalMSA.cdsP" );
unlink("$originalMSA.cdsP.html") if ( -z "$originalMSA.cdsP.html" );
unlink("$originalMSA.out") if ( -z "$originalMSA.out" );
unlink("$originalMSA.boj") if ( -z "$originalMSA.boj" || !-e "$originalMSA.cds" );
unlink("${originalMSA}.cds") if ( -z "${originalMSA}.cds" );
unlink("${originalMSA}.cdsP") if ( -z "${originalMSA}.cdsP" );
unlink("${originalMSA}.cdsP.html") if ( -z "${originalMSA}.cdsP.html" );
unlink("${originalMSA}.out") if ( -z "${originalMSA}.out" );
unlink("${originalMSA}.boj") if ( -z "${originalMSA}.boj" || !-e "${originalMSA}.cds" );
return;
}
########################################################
......@@ -1512,6 +1515,8 @@ sub template_failure {
print {*STDERR} "\t >CDK2_hs_G_My_Seq\n";
print {*STDERR} "\t TTCCTTCTCAGGGATAACACTCTATTCATGTCACTCCATTCA...\n";
print {*STDERR} "\t\tif you provide your own nucleotidic target sequence\n\n";
return;
}
sub checkTemplate {
......
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